JuliaHealth
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@def hasmath = true

These are the public notes for the JuliaHealth Community. Notes are published publicly here and are available for comments and review on the public HackMD. Additionally, the notes are hosted publicly on the GitHub and are open for PRs or edits as needed.

August 25 2023

In Attendance:

Location: Virtual (JuliaHealth Google Meet)

Summary:

Keywords:

Agenda

  1. New member introductions

  2. Running tasks follow-ups:

a. Short-term task follow-ups:

i. @Jacob Set-up HackMD to take notes going forward - Copy and paste meeting minutes over to JuliaHealth PR to update at end of meetings ii. @Dilum finds out how to live stream JuliaHealth BoF

b. Long-term task follow-ups:

i. Creating a template repository

  1. Debrief from JuliaCon

a. Interoperability of Julia with health research ecosystems (R)

b. Develop and document tutorials showcasing compositional solutions to JuliaHealth ecosystem problems

c. Coordinate with bigger Julia Blog to bridge between communities even better

d. Databases and JuliaHealth

  1. Open discussion on next steps for the JuliaHealth community

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Notes

July 28 2023

In Attendance: [Attendance Waived for In-Person Meeting

Location: JuliaCon 2023 JuliaHealth Birds of a Feather

Summary: New member backgrounds, problems within the Julia ecosystem related to healthcare, thoughts on addressing issues within a JuliaHealth context, and learning resources for Julia within the context of health.

Keywords: #ehr #genomics #biology #interoperability #database #sql #outreach

Agenda

  1. Introductions and what people in the community are using Julia for in health research

  2. What is missing of painful in Julia that is needed to drive health research forward

  3. Thoughts on how to address some of these problems

  4. Open discussion and next steps for JuliaHealth

Short-Term Outcomes

Not Available

Long-Term Outcomes

Meeting Notes

June 30 2023

Meeting Summary

In Attendance: Jacob Zelko, Fareeda Abdelazeez, Zachary Christensen

Location: Virtual

Summary: Discussed new members, upcoming JuliaCon, JuliaHealth Birds of a Feather discussion on topics like neural decoding and OMOP tooling, managing logistics for Julia organizations, and JuliaHealth PR reviews.

Keywords: #brain #imaging #neural #decoding #collaboration #community #engagement

Agenda

  1. New member welcomes!

  2. Planning JuliaHealth Birds of a Feather

    1. Topics?

    2. Facilitators?

    3. Creating actionable outcomes?

  3. Open discussion on Julia Orgs, How Do You Manage Logistics?

  4. Misc topics

  5. Julia for Health Informatics Research & Bridging community organizations

    1. Open Discussion on The Graphs Ecosystem

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Meeting Notes

May 26 2023

Meeting Summary

In Attendance: Jacob Zelko, Dilum Aluthge, Asher Wasserman, Fareeda Abdelazeez, Kyle Beggs

Location: Virtual

Summary: First JuliaHealth community call to meet other Julians, learn how we can galvanize the Juliahealth Community, and open discussion on paths forward

Keywords: #data #analysis #hemodynamics #omop #machine #learning

Agenda

  1. Introductions

  2. What people are using Julia for in health research

  3. Selected topics and state within the Julia ecosystem:

    1. Observational Health

    2. Medical Imaging

    3. Machine Learning and Health

    4. Interoperability Standards

    5. Drug Discovery

  4. Standard Interfaces

Meeting Outcomes

Short-Term Outcomes

Long-Term Outcomes

Meeting Notes

  1. Introductions

    1. Dilum Aluthge – MD/PhD Student Brown University (BCBI), PumasAI

      1. Julia Community Involvement

        1. Pkg

        2. General Registry

        3. Continuous Integration

      2. JuliaHealth and beyond

        1. Originally created JuliaHealth to bring people together in health

        2. BioJulia folks are a great source of inspiration for packages!

      3. Birds of a Feather!!! COME VISIT! – Friday July 28th, 4PM EST in Boston, MA!

    2. Asher Wasserman – Astronomy PhD, Data Scientist in BioTech

      1. Julia Community Involvement

        1. Differential Equations

        2. One off deployments

    3. Fareeda Abdelazeez – GSoC JuliaHealth (First GSoC Student!!!!!)

      1. Julia Community Involvement

        1. Observational Health tooling JuliaHealth!

    4. Kyle Beggs – Software Engineer in small Optics company, Finishing PhD in MechE

      1. Julia Community Involvement

        1. PDEs

        2. Hemodynamics research focus

        3. Take advantage of these tools for imaging, segmentation

  2. What people are using Julia for in health research

    1. Asher: Cancer patient data

      1. PDFs and other data formats 

        1. CDA documents

      2. How to structure this ad hoc type of data into common data model

      3. Developing processes to automatically make these documents useful

      4. How do we clean the data to match actual reality

      5. How do we make this data actionable/useful

      6. Could match towards goals of OHDSI/observational health

        1. Analyses at population level?

        2. Outcome propensity scores?

        3. Patient phenotype development?

      7. Role of Julia:

        1. Mainly as a scripting language

        2. Supplement to a lot of SQL scripting (FunSQL discovered)

        3. Python is generally being deployed because of software devs

          1. How to not crash AWS, etc.

        4. Julia deployment for risk (?)

        5. Survival Analysis in Julia; lifelines in Python otherwise

    2. Kyle: Vascular Surgical Planning

      1. Unobvious on where to place graft, etc – educated guesses

      2. Creating a tool to simulate operations

      3. Why Julia?

        1. Existing tools are open source but really GUI-driven

        2. Integration across ecosystem would be even better for hemodynamics in Julia

        3. Give a base to simulate the mechanics involved with this

          1. JuliaFEM, etc. 

      4. Mesh list methods

        1. Point clouds

        2. Main application is within hemodynamics

    3. Fareeda: JuliaHealth GSoC Student

      1. Working on OMOP Common Data Model

      2. Standard model for observational health patient data

      3. Develop infrastructure of JuliaHealth to work with OMOP CDM data

        1. Improve DBConnector

        2. OMOPCDMCohortCreator.jl – add tooling

        3. OHDSIAPI.jl – creating interfaces for ATHENA/ATLAS

      4. Patient Level Prediction tooling

        1. Using MLJ algorithms

        2. Attempting to solve a research question

          1. Evaluate success of package

      5. Stretch goals:

        1. Cohort Quality and underlying data is “good”

        2. Build support for OBDC connections

    4. Overlap with other organizations

      1. Doesn’t happen in a vacuum

      2. Serving as a bridge between a bridge and a community between other groups

      3. What should be JuliaHealth?

        1. Bringing together people 

  3. Selected topics and state within the Julia ecosystem:

    1. Observational Health

    2. Medical Imaging

    3. Machine Learning and Health

    4. Interoperability Standards

    5. Drug Discovery

  4. Standard Interfaces

June 30th, 2023

Attending:

Agenda:

  1. New member welcomes!

  2. Planning JuliaHealth Birds of a Feather

    1. Topics?

    2. Facilitators?

    3. Creating actionable outcomes?

  3. Open discussion on Julia Orgs, How Do You Manage Logistics?

  4. Misc topics

    1. Julia for Health Informatics Research & Bridging community organizations

      1. Open Discussion on The Graphs Ecosystem

Notes: 

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